666de878ad
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10558 f3b2605a-c512-4ea7-a41b-209d697bcdaa
119 lines
4.0 KiB
Plaintext
119 lines
4.0 KiB
Plaintext
# needs description
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# E = - grad \phi
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# f = q E
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# NOTE tangent is constant for LAGRANGIAN but not exact...
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# NOTE try one atom and one free node
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# issue is one of magnitude of E since
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# tangent = perm BB - dn/dphi NN
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# CHECK CONDITIONING?
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echo both
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units metal
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atom_style atomic
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lattice diamond 3.6
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boundary f f f
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#region box block -4.3458792459312239 4.3458792459312328 -4.3458792459312168 4.3458792459312203 0.0 104.29551668 units box
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#region box block 0 10 0 10 0 10
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#create_box 1 box
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#group box region box
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#atom_modify sort 0 1
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pair_style tersoff
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read_data tube_8_4.data
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pair_coeff * * ../../../../potentials/SiC.tersoff C
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mass * 12.01
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# PARAMETERS-----------------------------
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variable L equal zhi-zlo
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variable R equal 12.1/2
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variable xhiFE equal 5.0*$R
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variable xloFE equal -${xhiFE}
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variable yhiFE equal $R
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variable yloFE equal -${xhiFE}
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variable zhiFE equal zhi
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variable zloFE equal zlo+10
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print "Length $L [${zloFE}, ${zhiFE}]"
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variable E equal 0.01 # 1.0 10.0 0.01
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variable V equal $E*${zloFE}
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variable V equal 2
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print "Electric field $E ref.voltage $V"
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variable s equal 20
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# END -----------------------------------
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# all atoms simulation
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region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
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group internal region feRegion
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variable nAll equal count(all)
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variable nGhost equal count(all)-count(internal)
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print ">>> number of stationary ghosts: ${nGhost} of ${nAll}"
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#neighbor 5. bin
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#neigh_modify every 10 delay 0 check no
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timestep 0.0005
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# coupling
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fix AtC internal atc electrostatic-equilibrium CNT_electrostatic2.mat
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fix_modify AtC omit atomic_charge
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#fix_modify AtC internal_quadrature off <<<< ???
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variable alat equal 1.42
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variable w equal ${alat}*${alat}*3.*sqrt(3.)/4.0
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#variable w equal 10
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fix_modify AtC atom_weight constant internal $w
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fix_modify AtC source_integration atom
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fix_modify AtC atom_element_map eulerian 1
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fix_modify AtC mesh create 5 1 12 feRegion f p f
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fix_modify AtC control momentum flux
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#fix_modify AtC extrinsic poisson_solver max_iterations 5
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# initial conditions
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fix_modify AtC initial displacement x all 0.0
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fix_modify AtC initial displacement y all 0.0
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fix_modify AtC initial displacement z all 0.0
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fix_modify AtC initial velocity x all 0.0
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fix_modify AtC initial velocity y all 0.0
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fix_modify AtC initial velocity z all 0.0
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#variable a equal -$R-0.1
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#variable b equal $R+0.1
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#fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box
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fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box
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fix_modify AtC mesh create_nodeset rbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box
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fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
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fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box
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# boundary conditions
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fix_modify AtC fix displacement x lbc 0.
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fix_modify AtC fix displacement y lbc 0.
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fix_modify AtC fix displacement z lbc 0.
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fix_modify AtC fix velocity x lbc 0.
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fix_modify AtC fix velocity y lbc 0.
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fix_modify AtC fix velocity z lbc 0.
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fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
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#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
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##fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 $V
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fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 $V
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# run
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thermo_style custom step cpu etotal ke
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thermo $s
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fix_modify AtC output cnt_electrostatic2FE $s full_text # binary
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fix_modify AtC output index step
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# NOTE not recognized as vector by paraview
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variable uX atom x-f_AtC[1]
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variable uY atom y-f_AtC[2]
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variable uZ atom z-f_AtC[3]
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variable rho atom mass*f_AtC[4]
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dump CONFIG all custom $s cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho
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log cnt_electrostatic2.log
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#run $s
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run 100
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# NOTE try fix charge on tip
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